The City of Hope Functional Genomics Core encompasses the spotted microarray and the ligation-mediated polymerase chain reaction (LM-PCR) facilities. The Core's mission is to serve the genomics and proteomics needs of the City of Hope research community. Our immediate goals are to provide state of the art technology for production and analysis of spotted microarrays for gene expression profiling and to facilitate the study of gene promoters by providing automated LM-PCR service for in vivo footprinting. The Core's equipment was purchased with funds from private foundation contributions to City of Hope. The facility possesses liquid handling robots for processing cDNA clones in preparation for spotting, including a Biomek 2000 SL for barcode controlled handling of microtiter plates and pipetting. A CSS Packard Multiprobe II is available for equalization of cDNA concentrations and other procedures. Spotted microarrays are produced using a DeRisi version II arrayer assembled from robotic components at City of Hope. To assure quality synthesis and labeling of gene expression targets, analysis and quantitation of RNA samples are performed using an Agilent DNA/RNA Bioanalyzer. The results from hybridization experiments, performed using automated hybridization equipment, are analyzed using the laser Axon 4000B fluorescence scanner and a Genicon resonance light scattering scanner. The robotic capabilities enable the core to rapidly complete genomic and proteomic projects by providing glass slides to its users containing 40,000 spots or more per slide. Custom arrays are tailored to specific genomic or proteomic experiments. In addition, core personnel provide training in the performance of microarray and LM-PCR experiments. The core facility centralizes the first stages of data storage and retrieval utilizing a database developed as an open source software package by academics for the stated purpose of organizing and sharing gene expression profiling results. Data can then be exported for further analysis by our NASA Jet Propulsion Laboratory collaborators or as desired by individual investigators. For suppression subtractive hybridization protocols, the core maintains a database that aids in cataloging clones. Peer reviewed usage of this core by Cancer Center members is 76.25% of total usage.